Our class diagram is way out of date, but I believe the SearchIO part is still basically the same.
http://www.bioperl.org/wiki/Class_Diagram
> But I feel it would be much easier to see this relationship, if
> this is drawn graphically.
Absolutely. Speaking of which, this has long been on our to-do list — would you be interested in taking a crack at this?
There's also the Deobfuscator, which allows you to see all of the methods available to an object, regardless of how far up the inheritance tree the method originates:
http://www.bioperl.org/wiki/Deobfuscator
Dave